Calcium in PDB 8s3c: Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 (Unliganded)

The structure of Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 (Unliganded), PDB code: 8s3c was solved by M.Grzechowiak, M.Ruszkowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.83 / 2.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	95.651, 164.554, 195.412, 90, 90, 90
R / Rfree (%)	17.4 / 20.4

The structure of Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 (Unliganded) also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 (Unliganded) (pdb code 8s3c). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 (Unliganded), PDB code: 8s3c:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 (Unliganded)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 (Unliganded) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:47.6 occ:1.00 O B:HOH629 2.2 48.7 1.0 O B:ILE30 2.3 45.8 1.0 O B:SER27 2.4 53.0 1.0 O B:HOH612 2.5 49.6 1.0 C B:ILE30 3.5 51.4 1.0 C B:SER27 3.5 53.5 1.0 OG B:SER27 3.9 53.5 1.0 CA B:LEU28 4.2 55.7 1.0 CA B:ILE30 4.2 47.7 1.0 O B:LEU28 4.3 52.8 1.0 C B:LEU28 4.3 54.5 1.0 N B:ILE30 4.3 54.0 1.0 N B:LEU28 4.3 55.7 1.0 O B:HIS58 4.3 48.0 1.0 CB B:ILE30 4.4 49.4 1.0 O B:HOH607 4.4 50.5 1.0 CA B:SER27 4.4 51.2 1.0 C B:PRO31 4.4 46.9 1.0 N B:TYR32 4.5 43.1 1.0 OD2 B:ASP59 4.5 49.2 1.0 N B:PRO31 4.5 48.0 1.0 CA B:PRO31 4.6 46.9 1.0 O B:HOH676 4.8 51.5 1.0 O B:PRO31 4.8 45.5 1.0 CB B:SER27 4.8 52.6 1.0 N B:LEU29 5.0 54.9 1.0 CG2 B:ILE30 5.0 47.5 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 (Unliganded)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 (Unliganded) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca505 b:47.4 occ:1.00 OE1 B:GLU38 2.3 51.1 1.0 O B:HOH689 2.6 46.4 1.0 CD B:GLU38 3.4 52.0 1.0 OE2 B:GLU38 3.8 55.1 1.0 O B:HOH673 4.5 46.3 1.0 CG B:GLU38 4.6 49.8 1.0 CB B:GLU38 4.8 49.7 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 (Unliganded)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Medicago Truncatula Glutamate Dehydrogenase 2 (Unliganded) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca503 b:51.0 occ:1.00 OE1 C:GLU38 2.4 53.1 1.0 O C:HOH675 2.5 50.2 1.0 CD C:GLU38 3.5 58.2 1.0 OE2 C:GLU38 4.0 59.7 1.0 O C:HOH635 4.7 56.6 1.0 CG C:GLU38 4.8 52.7 1.0 CB C:GLU38 4.9 53.0 1.0

M.Grzechowiak, J.Sliwiak, A.Link, M.Ruszkowski. Legume-Type Glutamate Dehydrogenase: Structure, Activity, and Inhibition Studies. Int.J.Biol.Macromol. V. 278 34648 2024.
ISSN: ISSN 0141-8130
PubMed: 39142482
DOI: 10.1016/J.IJBIOMAC.2024.134648